The Chemicalize website from ChemAxon is gaining interest (1,2) and, likely, LOTS of users! Chemicalize is both a website for recognizing chemical names and converting to chemical structures as well as an integration path to their property prediction algorithms. Some basic testing of chemicalize shows that their chemical name detection and conversion to structures using either name to structure conversion (algorithmically) or name lookup (via dictionaries) is very good. Not perfect, but very good. Perfect chemical name lookups are impossible as the associated dictionaries grow every time a new natural product is found for example, or a new drug is released.

With ChemSpider we are more interested in the linking to the predicted property pages. For example, if you want to see the predicted properties for Penicillin visit here.


Now, with ChemSpider ChemAxon were kind enough (and I mean applaud them, acknowledge them and send flowers!!) to give us a way to pass through a structure and initiate the predictions on the Chemicalize site. This is tremendous news for you all! Under the properties Infobox we provide a list of properties from ACD/Labs, a list of properties from EPISuite, a list of experimental properties, sourced from various places and now, the link to Predict Properties using Chemicalize.


Clicking the tab for Predict Properties from ChemAxon display the link through to Chemicalize as shown below.

chemicalize So, now we have sets of prediction capabilities linked up to ChemSpider. The ACD/Labs predictions are pre-calculated and every time there is an update to the algorithms in theory we would have to recalculate across the database and publish. This would take weeks of time across the almost 25 million structures so it is not a frequent task. It is the same issue with EPISuite. With the Chemicalize integration however the predictions are live, on the structure at the time it is passed to the algorithms. This has the advantage that the prediction algorithms can be incrementally improved and you will always get the latest and greatest results. However, having the predicted values from ACD/Labs available allows flexible searching as shown below. We are grateful to ChemAxon to allowing us to integrate Chemicalize. It gives LIVE access to the latest and greatest predictions as well as access to a whole series of new predictions for which we don’t have data on the database…especially pKa values, topology analysis, geometry and others. Thanks ChemAxon!


Stumble it!

3 Responses to “ChemSpider Integrates Chemicalize”

  1. cdsouthan says:

    This is good but would be great if you could couple the chemicalize IUPAC > structure directly into a ChemSpider search.

  2. Antony Williams says:

    Chris…I think it’s a good idea too. Drop a note to Alex Allardyce and encourage the idea and I will chat with him this coming week at the Boston ACS meeting. Cheers

  3. Chris Swain says:

    If you will excuse the shameless plug. I’ve written a free extension for Safari that submits the current page to It is available here

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